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#!/usr/bin/env python
'''
Python Wrapper for a perl based program.
Generates tile based quality graphics
Output: pdf
@author: Manuel Kohler
@copyright: ETH Zurich
@precondition: Working pdftk and SolexaQA.pl binaries
'''
import subprocess
import shlex
import os
import sys
from optparse import OptionParser
SCRIPT = "/usr/local/dsu/bin/SolexaQA/SolexaQA.pl"
PDFTK = '/usr/local/dsu/pdftk-1.41/pdftk/pdftk'
parser = OptionParser()
parser.add_option("-p", "--path", dest="path", action="store", type="string",
help="Path of the fastq files", metavar="PATH")
parser.add_option("-v", dest="verbose", action="store_true",
help="tell me all")
(options, args) = parser.parse_args()
path = options.path
os.chdir(path)
listdir = os.listdir(path)
for file in listdir:
if file.endswith('fastq'):
args = SCRIPT + " -sanger " + path + "/" + file
Newargs = shlex.split(args)
p = subprocess.Popen(Newargs)
p.wait()
#convert -page A4 ETHZ_BSSE_110204_62Y8YAAXX_7.fastq.png ETHZ_BSSE_110204_62Y8YAAXX_7.fastq_TileStatistics_A4.pdf
convert = ['convert', '-page', 'A4', file + '.png', file + '.png.pdf']
c = subprocess.Popen(convert)
c.wait()
#rm *.matrix *.segments *.quality *.png
os.remove(file + '.matrix')
os.remove(file + '.segments')
os.remove(file + '.quality')
os.remove(file + '.png')
files = file + '.segments.hist.pdf', file + '.quality.pdf', file + '.png.pdf'
assemble = [ PDFTK, 'cat', 'output', file.replace('.', '_', 1) + '_SolexaQA.pdf']
[assemble.insert(1, i) for i in files]
a = subprocess.Popen(assemble)
a.wait()
[os.remove(f) for f in files]
print("Finished...")